Identifying the Lipidomic Effects of a Rare Loss-of-Function Deletion in ANGPTL3

Background: The identification and understanding of therapeutic targets for atherosclerotic cardiovascular disease is of fundamental importance given its global health and economic burden. Inhibition of ANGPTL3 (angiopoietin-like 3) has demonstrated a cardioprotective effect, showing promise for atherosclerotic cardiovascular disease treatment, and is currently the focus of ongoing clinical trials. Here, we assessed the genetic basis of variation in ANGPTL3 levels in the San Antonio Family Heart Study. Methods: We assayed ANGPTL3 protein levels in ≈1000 Mexican Americans from extended pedigrees. By drawing upon existing plasma lipidome profiles and genomic data we conducted analyses to understand the genetic basis to variation in ANGPTL3 protein levels, and accordingly the correlation with the plasma lipidome. Results: In a variance components framework, we identified that variation in ANGPTL3 was significantly heritable (h2=0.33, P=1.31×10-16). To explore the genetic basis of this heritability, we conducted a genome-wide linkage scan and identified significant linkage (logarithm of odds =6.18) to a locus on chromosome 1 at 90 centimorgans, corresponding to the ANGPTL3 gene location. In the genomes of 23 individuals from a single pedigree, we identified a loss-of-function variant, rs398122988 (N121Kfs*2), in ANGPTL3, that was significantly associated with lower ANGPTL3 levels (β=-1.69 SD units, P=3.367×10-13), and accounted for the linkage signal at this locus. Given the known role of ANGPTL3 as an inhibitor of endothelial and lipoprotein lipase, we explored the association of ANGPTL3 protein levels and rs398122988 with the plasma lipidome and related phenotypes, identifying novel associations with phosphatidylinositols. Conclusions: Variation in ANGPTL3 protein levels is heritable and under significant genetic control. Both ANGPTL3 levels and loss-of-function variants in ANGPTL3 have significant associations with the plasma lipidome. These findings further our understanding of ANGPTL3 as a therapeutic target for atherosclerotic cardiovascular disease

Rare DEGS1 variant significantly alters de novo ceramide synthesis pathway

The de novo ceramide synthesis pathway is essential to human biology and health but genetic influences remain unexplored. The core function of this pathway is the generation of biologically active ceramide from its precursor, dihydroceramide. Dihydroceramides have diverse, often protective, biological roles; conversely, increased ceramide levels are biomarkers of complex disease. To explore the genetics of the ceramide synthesis pathway, we searched for deleterious nonsynonymous variants in the genomes of 1,020 Mexican Americans from extended pedigrees. We identified a Hispanic ancestry−specific rare functional variant, L175Q, in DEGS1, a key enzyme in the pathway that converts dihydroceramide to ceramide. This amino acid change was significantly associated with large increases in plasma dihydroceramides. Indexes of DEGS1 enzymatic activity were dramatically reduced in heterozygotes. CRISPR/Cas9 genome editing of HepG2 cells confirmed that the L175Q variant results in a partial loss of function for the DEGS1 enzyme. Understanding the biological role of DEGS1 variants, such as L175Q, in ceramide synthesis may improve the understanding of metabolic-related disorders, and spur ongoing research of drug targets along this pathway

Early life risk factors of motor, cognitive and language development: a pooled analysis of studies from low/middle-income countries.

OBJECTIVE:To determine the magnitude of relationships of early life factors with child development in low/middle-income countries (LMICs). DESIGN:Meta-analyses of standardised mean differences (SMDs) estimated from published and unpublished data. DATA SOURCES:We searched Medline, bibliographies of key articles and reviews, and grey literature to identify studies from LMICs that collected data on early life exposures and child development. The most recent search was done on 4 November 2014. We then invited the first authors of the publications and investigators of unpublished studies to participate in the study. ELIGIBILITY CRITERIA FOR SELECTING STUDIES:Studies that assessed at least one domain of child development in at least 100 children under 7 years of age and collected at least one early life factor of interest were included in the study. ANALYSES:Linear regression models were used to assess SMDs in child development by parental and child factors within each study. We then produced pooled estimates across studies using random effects meta-analyses. RESULTS:We retrieved data from 21 studies including 20 882 children across 13 LMICs, to assess the associations of exposure to 14 major risk factors with child development. Children of mothers with secondary schooling had 0.14 SD (95% CI 0.05 to 0.25) higher cognitive scores compared with children whose mothers had primary education. Preterm birth was associated with 0.14 SD (-0.24 to -0.05) and 0.23 SD (-0.42 to -0.03) reductions in cognitive and motor scores, respectively. Maternal short stature, anaemia in infancy and lack of access to clean water and sanitation had significant negative associations with cognitive and motor development with effects ranging from -0.18 to -0.10 SDs. CONCLUSIONS:Differential parental, environmental and nutritional factors contribute to disparities in child development across LMICs. Targeting these factors from prepregnancy through childhood may improve health and development of children

Concordant changes of plasma and kidney microRNA in the early stages of acute kidney injury: time course in a mouse model of bilateral renal ischemia-reperfusion.

BACKGROUND: Acute kidney injury (AKI) is a syndrome characterized by the rapid loss of the kidney excretory function and is strongly associated with increased early and long-term patient morbidity and mortality. Early diagnosis of AKI is challenging; therefore we profiled plasma microRNA in an effort to identify potential diagnostic circulating markers of renal failure. The goal of the present study was to investigate the dynamic relationship of circulating and renal microRNA profiles within the first 24 hours after bilateral ischemia-reperfusion kidney injury in mice. METHODOLOGY/PRINCIPAL FINDINGS: Bilateral renal ischemia was induced in C57Bl/6 mice (n = 10 per group) by clamping the renal pedicle for 27 min. Ischemia-reperfusion caused highly reproducible, progressive, concordant elevation of miR-714, miR-1188, miR-1897-3p, miR-877*, and miR-1224 in plasma and kidneys at 3, 6 and 24 hours after acute kidney injury compared to the sham-operated mice (n = 5). These dynamics correlated with histologic findings of kidney injury and with a conventional plasma marker of renal dysfunction (creatinine). Pathway analysis revealed close association between miR-1897-3p and Nucks1 gene expression, which putative downstream targets include genes linked to renal injury, inflammation and apoptosis. CONCLUSIONS/SIGNIFICANCE: Systematic profiling of renal and plasma microRNAs in the early stages of experimental AKI provides the first step in advancing circulating microRNAs to the level of promising novel biomarkers

Changes of plasma creatinine in the time course of renal ischemia-reperfusion.

<p>Creatinine is a conventional circulating marker that is elevated when the kidney excretory function is impaired. In the sham-operated mice, plasma creatinine levels were at or below detection, while they were significantly increased in the animals that underwent bilateral renal ischemia-reperfusion. Plasma creatinine levels progressively grew over the time of reperfusion. Time points on the graph represent the time of reperfusion.</p

Correlation of plasma miR-1897-3p, miR-1188, and miR-714 with plasma creatinine.

<p>Correlation of plasma miR-1897-3p, miR-1188, and miR-714 with plasma creatinine.</p

MicroRNA expression confirmation by real-time PCR in the samples from individual animals.

<p>Eleven microRNA species were selected on the basis of concordant and discordant changes in the kidney and plasma as detected in the pooled samples. The changes in five microRNAs were confirmed in the samples from individual animals. Bars on graphs represent fold changes from the time-matched sham-operated animals. MicroRNA expression levels form the sham-operated animals (not shown on graphs) are set to 1. Panel A shows miR-714 changes in kidney and plasma. Panel B shows miR-1188. Panel C shows miR-1897-3p. Panel D shows miR-877*. Panel E shows miR-1224. Two sample t tests were performed on sham and ischemic groups at each timepoint, then p values were adjusted with Bonferroni correction. # = p<0.05; ## = p<0.01; ### = p<0.001.</p

Pattern of microRNA modulation in kidneys and plasma of mice undergoing ischemia-reperfusion.

<p>While multiple microRNA species were modulated in the kidneys and in plasma after ischemia-reperfusion, 18 microRNAs were modulated in both compartments in a time-dependent manner. <b>Up</b>, increased expression; <b>Down</b>, decreased expression; <b>Early</b>, modulated at 3 hours and returned to the Sham level at 24 hours.</p

Downstream targets of Nucks1.

<p>Pathway analysis was performed on Nucks1 (nuclear casein kinase and cyclin-dependent kinase substrate 1) using Ingenuity Pathway Analysis. Downstream targets of Nucks1 appear to be involved in renal injury, inflammation, and apoptosis.</p

Nucks1 expression in the kidneys of mice with renal ischemia-reperfusion.

<p>Nucks1 gene expression was down-regulated in the injured kidneys at all time points and reached significance at 3 and 24 hours after reperfusion.</p